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Merge branch 'lammps:develop' into fortran-tinkering

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hammondkd
2022-08-12 11:47:27 -05:00
committed by GitHub
parent 257b551c92 208caacb89
commit d1429d1b11
15 changed files with 222 additions and 166 deletions
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19
doc/src/Run_options.rst
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@ -14,6 +14,7 @@ letter abbreviation can be used:
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
* :ref:`-nb or -nonbuf <nonbuf>`
* :ref:`-pk or -package <package>`
* :ref:`-p or -partition <partition>`
* :ref:`-pl or -plog <plog>`
@ -257,6 +258,24 @@ Disable generating a citation reminder (see above) at all.
----------
.. _nonbuf:
**-nonbuf**
Turn off buffering for screen and logfile output. For performance
reasons, output to the screen and logfile is usually buffered, i.e.
output is only written to a file if its buffer - typically 4096 bytes -
has been filled. When LAMMPS crashes for some reason, however, that can
mean that there is important output missing. With this flag the
buffering can be turned off (only for screen and logfile output) and any
output will be committed immediately. Note that when running in
parallel with MPI, the screen output may still be buffered by the MPI
library and this cannot be changed by LAMMPS. This flag should only be
used for debugging and not for production simulations as the performance
impact can be significant, especially for large parallel runs.
----------
.. _package:
**-package style args ....**

2
examples/COUPLE/fortran2/LAMMPS.F90
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@ -1105,7 +1105,7 @@ contains !! Wrapper functions local to this module {{{1
C_xy = xy
C_xz = xz
C_yz = yz
call lammps_actual_reset_box (ptr, C_boxlo, C_boxhi, C_xy, C_xz, C_yz)
call lammps_actual_reset_box (ptr, C_boxlo, C_boxhi, C_xy, C_yz, C_xz)
end subroutine lammps_reset_box
! lammps_gather_atoms {{{2

18
examples/COUPLE/fortran2/README
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@ -40,7 +40,7 @@ the dynamically-linkable library (liblammps_fortran.so).
(2) Copy said library to your Fortran program's source directory or replace
${LAMMPS_LIB} with its full path in the instructions below.
(3) Compile (but don't link!) LAMMPS.F90. Example:
mpif90 -c LAMMPS.f90
mpifort -c LAMMPS.f90
OR
gfortran -c LAMMPS.F90
NOTE: you may get a warning such as,
@ -72,8 +72,8 @@ the dynamically-linkable library (liblammps_fortran.so).
were part of the usual LAMMPS library interface (if you have the module
file visible to the compiler, that is).
(6) Compile (but don't link) your Fortran program. Example:
mpif90 -c myfreeformatfile.f90
mpif90 -c myfixedformatfile.f
mpifort -c myfreeformatfile.f90
mpifort -c myfixedformatfile.f
OR
gfortran -c myfreeformatfile.f90
gfortran -c myfixedformatfile.f
@ -83,12 +83,12 @@ the dynamically-linkable library (liblammps_fortran.so).
IMPORTANT: If the Fortran module from part (3) is not in the current
directory or in one searched by the compiler for module files, you will
need to include that location via the -I flag to the compiler, like so:
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
(7) Link everything together, including any libraries needed by LAMMPS (such
as the C++ standard library, the C math library, the JPEG library, fftw,
etc.) For example,
mpif90 LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
mpifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
OR
gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
@ -105,17 +105,17 @@ You should now have a working executable.
(1) Compile LAMMPS as a dynamic library
(make makeshlib && make -f Makefile.shlib [targetname]).
(2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
mpif90 -fPIC -c LAMMPS.f90
mpifort -fPIC -c LAMMPS.f90
(3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
mpicxx -fPIC -c LAMMPS-wrapper.cpp
(4) Make the dynamic library, like so:
mpif90 -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
mpifort -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
(5) Compile your program, such as,
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
step (3)
(6) Link everything together, such as
mpif90 ${my_object_files} -L${LAMMPS_SRC} \
mpifort ${my_object_files} -L${LAMMPS_SRC} \
-L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
-llammps_openmpi -lmpi_cxx -lstdc++ -lm

70
examples/neb/in.neb.hop1
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@ -1,66 +1,66 @@
# 2d NEB surface simulation, hop from surface to become adatom
dimension 2
boundary p s p
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
variable u uloop 20
variable u uloop 20
# create geometry with flat surface
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
#create_box 3 box
#create_atoms 1 box
#mass * 1.0
#create_box 3 box
#create_atoms 1 box
#mass * 1.0
#write_data initial.hop1
read_data initial.hop1
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
# initial minimization to relax surface
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
timestep 0.05
timestep 0.05
# group of NEB atoms - either block or single atom ID 412
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal
fix 3 all enforce2d
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal
fix 3 all enforce2d
thermo 100
thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance
min_style quickmin
min_style quickmin
neb 0.0 0.1 1000 1000 100 final final.hop1
neb 0.0 0.1 1000 1000 100 final final.hop1

60
examples/neb/in.neb.hop1.end
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@ -1,56 +1,56 @@
# 2d NEB surface simulation, hop from surface to become adatom
dimension 2
boundary p s p
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
variable u uloop 20
variable u uloop 20
# create geometry with flat surface
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
read_data initial.hop1.end
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
timestep 0.05
timestep 0.05
# group of NEB atoms - either block or single atom ID 412
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
fix 3 all enforce2d
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
fix 3 all enforce2d
thermo 100
thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance
min_style quickmin
min_style quickmin
neb 0.0 0.1 1000 1000 100 final final.hop1
neb 0.0 0.1 1000 1000 100 final final.hop1

74
examples/neb/in.neb.hop2
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@ -1,68 +1,68 @@
# 2d NEB surface simulation, hop of adatom on surface
dimension 2
boundary p s p
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
variable u uloop 20
variable u uloop 20
# create geometry with adatom
lattice hex 0.9
region box block 0 20 0 11 -0.25 0.25
region box1 block 0 20 0 10 -0.25 0.25
lattice hex 0.9
region box block 0 20 0 11 -0.25 0.25
region box1 block 0 20 0 10 -0.25 0.25
#create_box 3 box
#create_atoms 1 region box1
#create_atoms 1 single 11.5 10.5 0
#mass * 1.0
#create_box 3 box
#create_atoms 1 region box1
#create_atoms 1 single 11.5 10.5 0
#mass * 1.0
#write_data initial.hop2
read_data initial.hop2
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
# initial minimization to relax surface
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
timestep 0.05
timestep 0.05
# group of NEB atoms - either block or single atom ID 421
region surround block 10 18 17 21 0 0 units box
group nebatoms region surround
#group nebatoms id 421
set group nebatoms type 3
group nonneb subtract all nebatoms
region surround block 10 18 17 21 0 0 units box
group nebatoms region surround
#group nebatoms id 421
set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0
fix 3 all enforce2d
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0
fix 3 all enforce2d
thermo 100
thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance
min_style fire
min_style fire
neb 0.0 0.05 1000 1000 100 final final.hop2
neb 0.0 0.05 1000 1000 100 final final.hop2

28
examples/neb/in.neb.sivac
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@ -5,7 +5,7 @@ units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
atom_modify sort 0 0.0
# coordination number cutoff
@ -45,7 +45,7 @@ group Si type 1
group del id 300
delete_atoms group del compress no
group vacneigh id 174 175 301 304 306 331 337
# choose potential
pair_style sw
@ -53,26 +53,26 @@ pair_coeff * * Si.sw Si
# set up neb run
variable u uloop 20
variable u uloop 20
# initial minimization to relax vacancy
displace_atoms all random 0.1 0.1 0.1 123456
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
# only output atoms near vacancy
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
# initial minimization to relax vacancy
fix 1 all neb 1.0
displace_atoms all random 0.1 0.1 0.1 123456
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
fix 1 all neb 1.0
thermo 100
thermo 100
# run NEB for 2000 steps or to force tolerance
timestep 0.01
min_style quickmin
min_style quickmin
neb 0.0 0.01 100 100 10 final final.sivac
neb 0.0 0.01 100 100 10 final final.sivac

26
python/lammps/mliap/__init__.py
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@ -4,17 +4,29 @@
# try to improperly start up a new interpreter.
import sysconfig
import ctypes
library = sysconfig.get_config_vars('INSTSONAME')[0]
import platform
py_ver = sysconfig.get_config_vars('VERSION')[0]
OS_name = platform.system()
if OS_name == "Linux":
SHLIB_SUFFIX = '.so'
library = 'libpython' + py_ver + SHLIB_SUFFIX
elif OS_name == "Darwin":
SHLIB_SUFFIX = '.dylib'
library = 'libpython' + py_ver + SHLIB_SUFFIX
elif OS_name == "Windows":
SHLIB_SUFFIX = '.dll'
library = 'python' + py_ver + SHLIB_SUFFIX
try:
pylib = ctypes.CDLL(library)
except OSError as e:
if pylib.endswith(".a"):
pylib.strip(".a") + ".so"
pylib = ctypes.CDLL(library)
else:
raise e
except Exception as e:
raise OSError("Unable to locate python shared library") from e
if not pylib.Py_IsInitialized():
raise RuntimeError("This interpreter is not compatible with python-based mliap for LAMMPS.")
del sysconfig, ctypes, library, pylib
from .loader import load_model, activate_mliappy

5
src/AMOEBA/amoeba_induce.cpp
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@ -369,7 +369,8 @@ void PairAmoeba::induce()
eps = DEBYE * sqrt(eps/atom->natoms);
if (eps < poleps) done = true;
if (eps > epsold) done = true;
// also commented out in induce.f of Tinker
// if (eps > epsold) done = true;
if (iter >= politer) done = true;
// apply a "peek" iteration to the mutual induced dipoles
@ -390,7 +391,7 @@ void PairAmoeba::induce()
// terminate the calculation if dipoles failed to converge
// NOTE: could make this an error
if (iter >= maxiter || eps > epsold)
if (iter >= politer || eps > epsold)
if (comm->me == 0)
error->warning(FLERR,"AMOEBA induced dipoles did not converge");
}

26
src/KOKKOS/kokkos.cpp
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@ -116,7 +116,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
while (iarg < narg) {
if (strcmp(arg[iarg],"d") == 0 || strcmp(arg[iarg],"device") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args");
device = atoi(arg[iarg+1]);
device = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"g") == 0 ||
@ -125,11 +125,11 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
error->all(FLERR,"GPUs are requested but Kokkos has not been compiled using a GPU-enabled backend");
#endif
if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args");
ngpus = atoi(arg[iarg+1]);
ngpus = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
int skip_gpu = 9999;
if (iarg+2 < narg && isdigit(arg[iarg+2][0])) {
skip_gpu = atoi(arg[iarg+2]);
skip_gpu = utils::inumeric(FLERR, arg[iarg+2], false, lmp);
iarg++;
}
iarg += 2;
@ -160,6 +160,12 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (device >= skip_gpu) device++;
set_flag = 1;
}
if ((str = getenv("PMI_LOCAL_RANK"))) {
int local_rank = atoi(str);
device = local_rank % ngpus;
if (device >= skip_gpu) device++;
set_flag = 1;
}
if (ngpus > 1 && !set_flag)
error->all(FLERR,"Could not determine local MPI rank for multiple "
@ -167,7 +173,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(arg[iarg],"t") == 0 ||
strcmp(arg[iarg],"threads") == 0) {
nthreads = atoi(arg[iarg+1]);
nthreads = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
if (nthreads <= 0)
error->all(FLERR,"Invalid number of threads requested for Kokkos: must be 1 or greater");
@ -176,19 +182,20 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(arg[iarg],"n") == 0 ||
strcmp(arg[iarg],"numa") == 0) {
numa = atoi(arg[iarg+1]);
numa = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
iarg += 2;
} else error->all(FLERR,"Invalid Kokkos command-line args");
} else error->all(FLERR,"Invalid Kokkos command-line arg: {}", arg[iarg]);
}
// Initialize Kokkos. However, we cannot change any
// Kokkos library parameters after the first initalization
if (args.num_threads != -1) {
if (args.num_threads != nthreads || args.num_numa != numa || args.device_id != device)
if ((args.num_threads != nthreads) || (args.num_numa != numa) || (args.device_id != device))
if (me == 0)
error->warning(FLERR,"Kokkos package already initalized, cannot reinitialize with different parameters");
error->warning(FLERR,"Kokkos package already initalized, "
"cannot reinitialize with different parameters");
nthreads = args.num_threads;
numa = args.num_numa;
device = args.device_id;
@ -200,8 +207,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
init_ngpus = ngpus;
}
if (me == 0)
utils::logmesg(lmp, " will use up to {} GPU(s) per node\n",ngpus);
if (me == 0) utils::logmesg(lmp, " will use up to {} GPU(s) per node\n", ngpus);
#ifdef LMP_KOKKOS_GPU
if (ngpus <= 0)

2
src/compute_pair_local.cpp
View File

@ -68,7 +68,7 @@ ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
pstyle[nvalues++] = DZ;
else if (arg[iarg][0] == 'p') {
int n = atoi(&arg[iarg][1]);
if (n <= 0) error->all(FLERR, "Invalid keyword in compute pair/local command");
if (n <= 0) error->all(FLERR, "Invalid keyword {} in compute pair/local command", arg[iarg]);
pstyle[nvalues] = PN;
pindex[nvalues++] = n - 1;

4
src/fmt/format.h
View File

@ -389,11 +389,11 @@ class uint128_fallback {
hi_ += (lo_ < n ? 1 : 0);
return *this;
}
#if FMT_HAS_BUILTIN(__builtin_addcll)
#if FMT_HAS_BUILTIN(__builtin_addcll) && !defined(__ibmxl__)
unsigned long long carry;
lo_ = __builtin_addcll(lo_, n, 0, &carry);
hi_ += carry;
#elif FMT_HAS_BUILTIN(__builtin_ia32_addcarryx_u64)
#elif FMT_HAS_BUILTIN(__builtin_ia32_addcarryx_u64) && !defined(__ibmxl__)
unsigned long long result;
auto carry = __builtin_ia32_addcarryx_u64(0, lo_, n, &result);
lo_ = result;

16
src/lammps.cpp
View File

@ -196,6 +196,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
int citelogfile = CiteMe::VERBOSE;
char *citefile = nullptr;
int helpflag = 0;
int nonbufflag = 0;
suffix = suffix2 = suffixp = nullptr;
suffix_enable = 0;
@ -298,6 +299,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
citeflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"-nonbuf") == 0 ||
strcmp(arg[iarg],"-nb") == 0) {
nonbufflag = 1;
iarg++;
} else if (strcmp(arg[iarg],"-package") == 0 ||
strcmp(arg[iarg],"-pk") == 0) {
if (iarg+2 > narg)
@ -520,7 +526,6 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
utils::flush_buffers(this);
}
// universe is one or more worlds, as setup by partition switch
// split universe communicator into separate world communicators
// set world screen, logfile, communicator, infile
@ -587,6 +592,15 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
}
}
// make all screen and logfile output unbuffered for debugging crashes
if (nonbufflag) {
if (universe->uscreen) setbuf(universe->uscreen, nullptr);
if (universe->ulogfile) setbuf(universe->ulogfile, nullptr);
if (screen) setbuf(screen, nullptr);
if (logfile) setbuf(logfile, nullptr);
}
// screen and logfile messages for universe and world
if ((universe->me == 0) && (!helpflag)) {

3
src/reader_xyz.cpp
View File

@ -179,8 +179,7 @@ void ReaderXYZ::read_atoms(int n, int nfield, double **fields)
++nid;
rv = sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz);
if (rv != 3)
error->one(FLERR,"Dump file is incorrectly formatted");
if (rv != 3) error->one(FLERR,"Dump file is incorrectly formatted");
// XXX: we could insert an element2type translation here
// XXX: for now we flag unrecognized types as type 0,

35
tools/python/pizza/dump.py
View File

@ -189,16 +189,26 @@ import sys, re, glob, types
from os import popen
from math import * # any function could be used by set()
try:
import numpy as np
oldnumeric = False
except:
import Numeric as np
oldnumeric = True
import numpy as np
try: from DEFAULTS import PIZZA_GUNZIP
except: PIZZA_GUNZIP = "gunzip"
# --------------------------------------------------------------------
# wrapper to convert old style comparision function to key function
def cmp2key(oldcmp):
class keycmp:
def __init__(self, obj, *args):
self.obj = obj
def __lt__(self, other):
return oldcmp(self.obj,other.obj) < 0
def __gt__(self, other):
return oldcmp(self.obj,other.obj) > 0
def __eq__(self, other):
return oldcmp(self.obj,other.obj) == 0
return keycmp
# Class definition
class dump:
@ -260,7 +270,7 @@ class dump:
# sort entries by timestep, cull duplicates
self.snaps.sort(self.compare_time)
self.snaps.sort(key=cmp2key(self.compare_time))
self.cull()
self.nsnaps = len(self.snaps)
print("read %d snapshots" % self.nsnaps)
@ -379,10 +389,7 @@ class dump:
for i in range(1,snap.natoms):
words += f.readline().decode().split()
floats = map(float,words)
if oldnumeric:
atom_data = np.array(list(floats),np.Float)
else:
atom_data = np.array(list(floats),np.float)
atom_data = np.array(list(floats),np.float)
snap.atoms = atom_data.reshape((snap.natoms, ncol))
else:
@ -858,8 +865,7 @@ class dump:
self.map(ncol+1,str)
for snap in self.snaps:
atoms = snap.atoms
if oldnumeric: newatoms = np.zeros((snap.natoms,ncol+1),np.Float)
else: newatoms = np.zeros((snap.natoms,ncol+1),np.float)
newatoms = np.zeros((snap.natoms,ncol+1),np.float)
newatoms[:,0:ncol] = snap.atoms
snap.atoms = newatoms
@ -1018,8 +1024,7 @@ class dump:
# convert values to int and absolute value since can be negative types
if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int)
else: bondlist = np.zeros((nbonds,4),np.int)
bondlist = np.zeros((nbonds,4),np.int)
ints = [abs(int(value)) for value in words]
start = 0
stop = 4